Australia's highest profile unionist, Paul Howes, has broken ranks with his own union and now supports Labor and unions severing their historic link.

Speaking on Sky TV on Monday, Mr Howes would not be drawn on his views saying he did not want to offer a running commentary. It was up to the union to have those debates in the future, he said.

However Fairfax Media understands Mr Howes has recently shifted position and now supports the cutting of the 123-year old formal tie between unions and Labor. The Australian Workers Union confirmed Mr Howes' resignation as national secretary on Monday. He will step down in July.

Recent scandals around the ALP-affiliated Health Services Union and ongoing controversies around his own union have focused attention on the Labor-union relationship.

So too has Labor's record low primary vote and the unions movement's declining membership and relevance.

In behind-the-scenes discussions the young leader has recently revealed his personal conclusion that affiliation was damaging both the party and affiliated unions. However he has been hamstrung in his public comments by the fact that AWU's official position was at odds with his personal view.

Once public, Mr Howes position will no doubt refuel debate about the need for reform.

Mr Howes has been national secretary of the AWU since 2007, replacing Bill Shorten. He was just 26 when he took on the role.

In a statement from the AWU this morning Mr Howes said: "I have spent half my life as an official in the trade union movement and the last seven years in this position.

I have always been aware that you never own this job; you only serve as custodian."

He denied he was leaving the AWU for a career in politics. "And so, despite what you may hear, I am not leaving this job to pursue a seat in parliament," he said. "For some time now I have been contemplating the next steps in my life. And as such I recognise the right thing to do is to step down."

Mr Howes, is engaged to Qantas executive Olivia Wirth and has, since announcing their relationship, been unwilling to comment on issues relating to the airline – in which his union has hundreds of members. Mr Howes and Ms Wirth will marry next month.

In September last year, Mr Howes pulled out of a bid to take a Senate seat to be vacated after the 2013 election by former foreign minister Bob Carr after hostile reaction from some Labor MPs and union figures.

But ALP insiders do not rule out Mr Howes seeking preselection in the future.

Mr Howes' relationship with Mr Shorten, now the Labor Opposition Leader, was damaged after Mr Shorten switched support to Mr Rudd before the 2013 federal poll.

The union leader also enraged many in the union movement in February when he called for a "grand compact" between unions and business in a speech that also created a political headache for Mr Shorten.

It is expected that Mr Howes will be replaced by assistant national secretary Scott McDine. He leaves the union movement as the Abbott government launches a royal commission into union corruption. The AWU is one of five unions singled out for special attention in the royal commission.

Set to be probed is the 20 year old scandal around a slush fund that involved legal work done by Julia Gillard for her then partner, AWU official Bruce Wilson. Also set to be investigated is a more recent slush fund, Industry 2020, set up by the union's former Victorian secretary and now state upper house MP, Cesar Melhem.

Often touted as a "faceless man", Mr Howes support for former prime minister Julia Gillard was instrumental in her toppling of Kevin Rudd in June 2010. He stayed loyal to Australia's first female PM in her leadership battles with Mr Rudd.

In November 2010, Mr Howes wrote Confessions of a Faceless Man: Inside Campaign 2010, an autobiographical analysis of the election and 18 months in Australian politics.